we have several servers colocated with several ISP's
i am trying to sort out some configuration that would ensure good uptime for
customers

We're helping a customer with a similar situation. They have multiple
incoming Internet connections. What we plan to do:
- Have a DNS server for each Internet connection
- Servers are replicated/available via every connection
- Each DNS server gives out IPs only within it's subnet
This way if one of the connections go down, that DNS server becomes available
and those IPs stop being handed out ... effectively removing those IPs from
your DNS rotation and automatically failing over to the remaining
connections. This also provides a load balancing effect.
Fraser

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Do you then have the root servers pointing to "all" of the DNS servers?
Have you modified the cache/ttl times to compensate for outages and
rollovers?

My understanding of the way DNS works, is that when a query hits the
root servers, they throw back any authoritative nameserver(s). The
requesting client then queries "one" nameserver. If it is unavailable,
it doesn't then query the other one(s). It times out. There is, to my
knowledge, no way to specify which DNS server the requesting client will
query. which would lead to clients attempting to query the server on the
downed link, and timing out. Or am I wrong?

Isn't the kind of situation that bgp or other dynamic routing protocols
were designed for?